class TestCyclicThermo(unittest.TestCase):
"""
Contains unit tests of the ThermoDatabase class.
"""
database = ThermoDatabase()
database.load(os.path.join(settings['database.directory'], 'thermo'))
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.database = self.__class__.database
def testComputeGroupAdditivityThermoForTwoRingMolecule(self):
"""
The molecule being tested has two rings, one is 13cyclohexadiene5methylene
the other is benzene ring. This method is to test thermo estimation will
give two different corrections accordingly.
"""
spec = Species().fromSMILES('CCCCCCCCCCCC(CC=C1C=CC=CC1)c1ccccc1')
spec.generateResonanceIsomers()
thermo = self.database.getThermoDataFromGroups(spec)
ringGroups, polycyclicGroups = self.database.getRingGroupsFromComments(
thermo)
self.assertEqual(len(ringGroups), 2)
self.assertEqual(len(polycyclicGroups), 0)
expected_matchedRingsLabels = ['13cyclohexadiene5methylene', 'Benzene']
expected_matchedRings = [
self.database.groups['ring'].entries[label]
for label in expected_matchedRingsLabels
]
self.assertEqual(set(ringGroups), set(expected_matchedRings))
def testThermoForMonocyclicAndPolycyclicSameMolecule(self):
"""
Test a molecule that has both a polycyclic and a monocyclic ring in the same molecule
"""
spec = Species().fromSMILES('C(CCC1C2CCC1CC2)CC1CCC1')
spec.generateResonanceIsomers()
thermo = self.database.getThermoDataFromGroups(spec)
ringGroups, polycyclicGroups = self.database.getRingGroupsFromComments(
thermo)
self.assertEqual(len(ringGroups), 1)
self.assertEqual(len(polycyclicGroups), 1)
expected_matchedRingsLabels = ['Cyclobutane']
expected_matchedRings = [
self.database.groups['ring'].entries[label]
for label in expected_matchedRingsLabels
]
self.assertEqual(set(ringGroups), set(expected_matchedRings))
expected_matchedPolyringsLabels = ['s3_5_5_ane']
expected_matchedPolyrings = [
self.database.groups['polycyclic'].entries[label]
for label in expected_matchedPolyringsLabels
]
self.assertEqual(set(polycyclicGroups), set(expected_matchedPolyrings))
def testGetRingGroupsFromComments(self):
"""
Test that getRingGroupsFromComments method works for fused polycyclics.
"""
from rmgpy.thermo.thermoengine import generateThermoData
# set-up RMG object
rmg = RMG()
# load kinetic database and forbidden structures
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.loadThermo(os.path.join(path, 'thermo'))
smi = 'C12C(C3CCC2C3)C4CCC1C4' #two norbornane rings fused together
spc = Species().fromSMILES(smi)
spc.thermo = generateThermoData(spc)
thermodb = rmg.database.thermo
thermodb.getRingGroupsFromComments(spc.thermo)
import rmgpy.data.rmg
rmgpy.data.rmg.database = None
def testRemoveGroup(self):
"""
Test that removing groups using nodes near the root of radical.py
"""
#load up test data designed for this test
database2 = ThermoDatabase()
path = os.path.join(os.path.dirname(rmgpy.__file__), 'data/test_data/')
database2.load(os.path.join(path, 'thermo'), depository=False)
#load up the thermo radical database as a test
radGroup = database2.groups['radical']
#use root as removed groups parent, which should be an LogicOr node
root = radGroup.top[0]
#use group to remove as
groupToRemove = radGroup.entries['RJ']
children = groupToRemove.children
#remove the group
radGroup.removeGroup(groupToRemove)
#afterwards groupToRemove should not be in the database or root's children
self.assertFalse(groupToRemove in radGroup.entries.values())
self.assertFalse(groupToRemove in root.children)
for child in children:
#groupToRemove children should all be in roots item.component and children attribuetes
self.assertTrue(child.label in root.item.components)
self.assertTrue(child in root.children)
#the children should all have root a their parent now
self.assertTrue(child.parent is root)
#Specific to ThermoDatabase, (above test apply to all base class Database)
#we check that unicode entry.data pointers are correctly reassigned
#if groupToRemove is a pointer and another node pointed to it, we copy
#groupToRemove pointer
self.assertTrue(radGroup.entries['OJ'].data is groupToRemove.data)
#Remove an entry with a ThermoData object
groupToRemove2 = radGroup.entries['CsJ']
radGroup.removeGroup(groupToRemove2)
#If groupToRemove was a data object, we point toward parent instead
self.assertTrue(radGroup.entries['RJ2_triplet'].data ==
groupToRemove2.parent.label)
#If the parent pointed toward groupToRemove, we need should have copied data object
Tlist = [300, 400, 500, 600, 800, 1000, 1500]
self.assertFalse(isinstance(groupToRemove2.parent.data, basestring))
self.assertTrue(
groupToRemove2.parent.data.getEnthalpy(298) ==
groupToRemove2.data.getEnthalpy(298))
self.assertTrue(
groupToRemove2.parent.data.getEntropy(298) ==
groupToRemove2.data.getEntropy(298))
self.assertFalse(False in [
groupToRemove2.parent.data.getHeatCapacity(x) ==
groupToRemove2.data.getHeatCapacity(x) for x in Tlist
])
def testIsPolyringPartialMatched(self):
# create testing molecule
smiles = 'C1CC2CCCC3CCCC(C1)C23'
mol = Molecule().fromSMILES(smiles)
polyring = [atom for atom in mol.atoms if atom.isNonHydrogen()]
# create matched group
matched_group = self.database.groups['polycyclic'].entries[
'PolycyclicRing'].item
# test
self.assertTrue(isPolyringPartialMatched(polyring, matched_group))
def testAddPolyRingCorrectionThermoDataFromHeuristicUsingPyrene(self):
# create testing molecule: Pyrene with two ring of aromatic version
# the other two ring of kekulized version
#
# creating it seems not natural in RMG, that's because
# RMG cannot parse the adjacencyList of that isomer correctly
# so here we start with pyrene radical and get the two aromatic ring isomer
# then saturate it.
smiles = '[C]1C=C2C=CC=C3C=CC4=CC=CC=1C4=C23'
spe = Species().fromSMILES(smiles)
spe.generateResonanceIsomers()
mols = []
for mol in spe.molecule:
sssr0 = mol.getSmallestSetOfSmallestRings()
aromaticRingNum = 0
for sr0 in sssr0:
sr0mol = Molecule(atoms=sr0)
if isAromaticRing(sr0mol):
aromaticRingNum += 1
if aromaticRingNum == 2:
mol.saturate()
mols.append(mol)
ringGroupLabels = []
polycyclicGroupLabels = []
for mol in mols:
polyring = mol.getDisparateRings()[1][0]
thermoData = ThermoData(
Tdata=([300, 400, 500, 600, 800, 1000, 1500], "K"),
Cpdata=([0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "J/(mol*K)"),
H298=(0.0, "kJ/mol"),
S298=(0.0, "J/(mol*K)"),
)
self.database._ThermoDatabase__addPolyRingCorrectionThermoDataFromHeuristic(
thermoData, polyring)
ringGroups, polycyclicGroups = self.database.getRingGroupsFromComments(
thermoData)
ringGroupLabels += [ringGroup.label for ringGroup in ringGroups]
polycyclicGroupLabels += [
polycyclicGroup.label for polycyclicGroup in polycyclicGroups
]
self.assertIn('Benzene', ringGroupLabels)
self.assertIn('six-inringtwodouble-12', ringGroupLabels)
self.assertIn('Cyclohexene', ringGroupLabels)
self.assertIn('1,3-Cyclohexadiene', ringGroupLabels)
self.assertIn('s2_6_6_ben_ene_1', polycyclicGroupLabels)
self.assertIn('s2_6_6_ben_ene_2', polycyclicGroupLabels)
self.assertIn('s2_6_6_naphthalene', polycyclicGroupLabels)
def testAddPolyRingCorrectionThermoDataFromHeuristicUsingAromaticTricyclic(
self):
# create testing molecule
#
# creating it seems not natural in RMG, that's because
# RMG cannot parse the adjacencyList of that isomer correctly
# so here we start with kekulized version and generateResonanceIsomers
# and pick the one with two aromatic rings
smiles = 'C1=CC2C=CC=C3C=CC(=C1)C=23'
spe = Species().fromSMILES(smiles)
spe.generateResonanceIsomers()
for mol in spe.molecule:
sssr0 = mol.getSmallestSetOfSmallestRings()
aromaticRingNum = 0
for sr0 in sssr0:
sr0mol = Molecule(atoms=sr0)
if isAromaticRing(sr0mol):
aromaticRingNum += 1
if aromaticRingNum == 2:
break
# extract polyring from the molecule
polyring = mol.getDisparateRings()[1][0]
thermoData = ThermoData(
Tdata=([300, 400, 500, 600, 800, 1000, 1500], "K"),
Cpdata=([0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "J/(mol*K)"),
H298=(0.0, "kJ/mol"),
S298=(0.0, "J/(mol*K)"),
)
self.database._ThermoDatabase__addPolyRingCorrectionThermoDataFromHeuristic(
thermoData, polyring)
ringGroups, polycyclicGroups = self.database.getRingGroupsFromComments(
thermoData)
ringGroupLabels = [ringGroup.label for ringGroup in ringGroups]
polycyclicGroupLabels = [
polycyclicGroup.label for polycyclicGroup in polycyclicGroups
]
self.assertIn('Benzene', ringGroupLabels)
self.assertIn('Cyclopentene', ringGroupLabels)
self.assertIn('s2_5_6_indene', polycyclicGroupLabels)
self.assertIn('s2_6_6_naphthalene', polycyclicGroupLabels)
def testAddPolyRingCorrectionThermoDataFromHeuristicUsingAlkaneTricyclic(
self):
# create testing molecule
smiles = 'C1CC2CCCC3C(C1)C23'
mol = Molecule().fromSMILES(smiles)
# extract polyring from the molecule
polyring = mol.getDisparateRings()[1][0]
thermoData = ThermoData(
Tdata=([300, 400, 500, 600, 800, 1000, 1500], "K"),
Cpdata=([0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "J/(mol*K)"),
H298=(0.0, "kJ/mol"),
S298=(0.0, "J/(mol*K)"),
)
self.database._ThermoDatabase__addPolyRingCorrectionThermoDataFromHeuristic(
thermoData, polyring)
ringGroups, polycyclicGroups = self.database.getRingGroupsFromComments(
thermoData)
ringGroupLabels = [ringGroup.label for ringGroup in ringGroups]
polycyclicGroupLabels = [
polycyclicGroup.label for polycyclicGroup in polycyclicGroups
]
self.assertIn('Cyclohexane', ringGroupLabels)
self.assertIn('Cyclopropane', ringGroupLabels)
self.assertIn('s2_6_6_ane', polycyclicGroupLabels)
self.assertIn('s2_3_6_ane', polycyclicGroupLabels)
class TestCyclicThermo(unittest.TestCase):
"""
Contains unit tests of the ThermoDatabase class.
"""
database = ThermoDatabase()
database.load(os.path.join(settings['database.directory'], 'thermo'))
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.database = self.__class__.database
def testComputeGroupAdditivityThermoForTwoRingMolecule(self):
"""
The molecule being tested has two rings, one is 13cyclohexadiene5methylene
the other is benzene ring. This method is to test thermo estimation will
give two different corrections accordingly.
"""
spec = Species().fromSMILES('CCCCCCCCCCCC(CC=C1C=CC=CC1)c1ccccc1')
spec.generateResonanceIsomers()
thermo = self.database.getThermoDataFromGroups(spec)
ringGroups, polycyclicGroups = self.database.getRingGroupsFromComments(
thermo)
self.assertEqual(len(ringGroups), 2)
self.assertEqual(len(polycyclicGroups), 0)
expected_matchedRingsLabels = ['13cyclohexadiene5methylene', 'Benzene']
expected_matchedRings = [
self.database.groups['ring'].entries[label]
for label in expected_matchedRingsLabels
]
self.assertEqual(set(ringGroups), set(expected_matchedRings))
def testThermoForMonocyclicAndPolycyclicSameMolecule(self):
"""
Test a molecule that has both a polycyclic and a monocyclic ring in the same molecule
"""
spec = Species().fromSMILES('C(CCC1C2CCC1CC2)CC1CCC1')
spec.generateResonanceIsomers()
thermo = self.database.getThermoDataFromGroups(spec)
ringGroups, polycyclicGroups = self.database.getRingGroupsFromComments(
thermo)
self.assertEqual(len(ringGroups), 1)
self.assertEqual(len(polycyclicGroups), 1)
expected_matchedRingsLabels = ['Cyclobutane']
expected_matchedRings = [
self.database.groups['ring'].entries[label]
for label in expected_matchedRingsLabels
]
self.assertEqual(set(ringGroups), set(expected_matchedRings))
expected_matchedPolyringsLabels = ['norbornane']
expected_matchedPolyrings = [
self.database.groups['polycyclic'].entries[label]
for label in expected_matchedPolyringsLabels
]
self.assertEqual(set(polycyclicGroups), set(expected_matchedPolyrings))
def testPolycyclicPicksBestThermo(self):
"""
Test that RMG prioritizes thermo correctly and chooses the thermo from the isomer which
has a non generic polycyclic ring correction
"""
spec = Species().fromSMILES('C1=C[C]2CCC=C2C1')
spec.generateResonanceIsomers()
thermoDataList = []
for molecule in spec.molecule:
thermo = self.database.estimateRadicalThermoViaHBI(
molecule, self.database.computeGroupAdditivityThermo)
thermoDataList.append(thermo)
thermoDataList.sort(key=lambda x: x.getEnthalpy(298))
most_stable_thermo = thermoDataList[0]
ringGroups, polycyclicGroups = self.database.getRingGroupsFromComments(
most_stable_thermo)
selected_thermo = self.database.getThermoDataFromGroups(spec)
self.assertNotEqual(selected_thermo, thermoDataList)
selected_ringGroups, selected_polycyclicGroups = self.database.getRingGroupsFromComments(
selected_thermo)
# The group used to estimate the most stable thermo is the generic polycyclic group and
# therefore is not selected. Note that this unit test will have to change if the correction is fixed later.
self.assertEqual(polycyclicGroups[0].label, 'PolycyclicRing')
self.assertEqual(selected_polycyclicGroups[0].label, 'C12CCC=C1CC=C2')
def testGetRingGroupsFromComments(self):
"""
Test that getRingGroupsFromComments method works for fused polycyclics.
"""
# set-up RMG object
rmg = RMG()
# load kinetic database and forbidden structures
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.loadThermo(os.path.join(path, 'thermo'))
smi = 'C12C(C3CCC2C3)C4CCC1C4' #two norbornane rings fused together
spc = Species().fromSMILES(smi)
spc.generateThermoData(rmg.database)
thermodb = rmg.database.thermo
thermodb.getRingGroupsFromComments(spc.thermo)
import rmgpy.data.rmg
rmgpy.data.rmg.database = None
class TestThermoDatabase(unittest.TestCase):
"""
Contains unit tests of the ThermoDatabase class.
"""
# Only load these once to save time
database = ThermoDatabase()
database.load(os.path.join(settings['database.directory'], 'thermo'))
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.database = self.__class__.database
# self.oldDatabase = self.__class__.oldDatabase
self.Tlist = [300, 400, 500, 600, 800, 1000, 1500]
self.testCases = [
# SMILES symm H298 S298 Cp300 Cp400 Cp500 Cp600 Cp800 Cp1000 Cp1500
# 1,3-hexadiene decomposition products
[
'C=CC=CCC', 3, 13.45, 86.37, 29.49, 37.67, 44.54, 50.12, 58.66,
64.95, 74.71
],
[
'[CH]=CC=CCC', 3, 72.55, 87.76, 29.30, 36.92, 43.18, 48.20,
55.84, 61.46, 70.18
],
[
'C=[C]C=CCC', 3, 61.15, 87.08, 29.68, 36.91, 43.03, 48.11,
55.96, 61.78, 71.54
],
[
'C=C[C]=CCC', 3, 61.15, 87.08, 29.68, 36.91, 43.03, 48.11,
55.96, 61.78, 71.54
],
[
'C=CC=[C]CC', 3, 70.35, 88.18, 29.15, 36.46, 42.6, 47.6, 55.32,
61.04, 69.95
],
[
'C=CC=C[CH]C', 6, 38.24, 84.41, 27.79, 35.46, 41.94, 47.43,
55.74, 61.92, 71.86
],
[
'C=CC=CC[CH2]', 2, 62.45, 89.78, 28.72, 36.31, 42.63, 47.72,
55.50, 61.21, 70.05
],
[
'[CH3]', 6, 34.81, 46.37, 9.14, 10.18, 10.81, 11.34, 12.57,
13.71, 15.2
],
[
'C=CC=C[CH2]', 2, 46.11, 75.82, 22.54, 28.95, 34.24, 38.64,
45.14, 49.97, 57.85
],
[
'[CH2]C', 6, 28.6, 59.87, 11.73, 14.47, 17.05, 19.34, 23.02,
25.91, 31.53
],
[
'C=CC=[CH]', 1, 85.18, 69.37, 18.93, 23.55, 27.16, 29.92,
34.02, 37.03, 41.81
],
[
'C=[CH]', 1, 71.62, 56.61, 10.01, 11.97, 13.66, 15.08, 17.32,
19.05, 21.85
],
[
'[CH]=CCC', 3, 58.99, 75.0, 20.38, 25.34, 29.68, 33.36, 39.14,
43.48, 50.22
],
# Cyclic Structures
[
'C1CCCCC1', 12, -29.45, 69.71, 27.20, 37.60, 46.60, 54.80,
67.50, 76.20, 88.50
],
[
'C1CCC1', 8, 6.51, 63.35, 17.39, 23.91, 29.86, 34.76, 42.40,
47.98, 56.33
],
[
'C1C=CC=C1', 2, 32.5, 65.5, 18.16, 24.71, 30.25, 34.7, 41.25,
45.83, 52.61
],
]
@work_in_progress
def testNewThermoGeneration(self):
"""
Test that the new ThermoDatabase generates appropriate thermo data.
"""
for smiles, symm, H298, S298, Cp300, Cp400, Cp500, Cp600, Cp800, Cp1000, Cp1500 in self.testCases:
Cplist = [Cp300, Cp400, Cp500, Cp600, Cp800, Cp1000, Cp1500]
molecule = Molecule(SMILES=smiles)
species = Species(molecule=molecule)
species.generateResonanceIsomers()
species.molecule[0]
thermoData = self.database.getThermoDataFromGroups(species)
molecule = species.molecule[0]
for mol in species.molecule[1:]:
thermoData0 = self.database.getAllThermoData(
Species(molecule=[mol]))[0][0]
for data in self.database.getAllThermoData(
Species(molecule=[mol]))[1:]:
if data.getEnthalpy(298) < thermoData0.getEnthalpy(298):
thermoData0 = data
if thermoData0.getEnthalpy(298) < thermoData.getEnthalpy(298):
thermoData = thermoData0
molecule = mol
self.assertAlmostEqual(H298,
thermoData.getEnthalpy(298) / 4184,
places=1,
msg="H298 error for {0}".format(smiles))
self.assertAlmostEqual(S298,
thermoData.getEntropy(298) / 4.184,
places=1,
msg="S298 error for {0}".format(smiles))
for T, Cp in zip(self.Tlist, Cplist):
self.assertAlmostEqual(Cp,
thermoData.getHeatCapacity(T) / 4.184,
places=1,
msg="Cp{1} error for {0}".format(
smiles, T))
def testSymmetryContributionRadicals(self):
"""
Test that the symmetry contribution is correctly added for radicals
estimated via the HBI method.
"""
spc = Species(molecule=[Molecule().fromSMILES('[CH3]')])
thermoData_lib = self.database.getThermoDataFromLibraries(spc)[0]
thermoData_ga = self.database.getThermoDataFromGroups(spc)
self.assertAlmostEqual(thermoData_lib.getEntropy(298.),
thermoData_ga.getEntropy(298.), 0)
@work_in_progress
def testSymmetryNumberGeneration(self):
"""
Test we generate symmetry numbers correctly.
This uses the new thermo database to generate the H298, used
to select the stablest resonance isomer.
"""
for smiles, symm, H298, S298, Cp300, Cp400, Cp500, Cp600, Cp800, Cp1000, Cp1500 in self.testCases:
molecule = Molecule(SMILES=smiles)
species = Species(molecule=molecule)
species.generateResonanceIsomers()
thermoData = self.database.getThermoDataFromGroups(
Species(molecule=[species.molecule[0]]))
# pick the molecule with lowest H298
molecule = species.molecule[0]
for mol in species.molecule[1:]:
thermoData0 = self.database.getAllThermoData(
Species(molecule=[mol]))[0][0]
for data in self.database.getAllThermoData(
Species(molecule=[mol]))[1:]:
if data.getEnthalpy(298) < thermoData0.getEnthalpy(298):
thermoData0 = data
if thermoData0.getEnthalpy(298) < thermoData.getEnthalpy(298):
thermoData = thermoData0
molecule = mol
self.assertEqual(
molecule.calculateSymmetryNumber(),
symm,
msg="Symmetry number error for {0}".format(smiles))
# @work_in_progress
# def testOldThermoGeneration(self):
# """
# Test that the old ThermoDatabase generates relatively accurate thermo data.
# """
# for smiles, symm, H298, S298, Cp300, Cp400, Cp500, Cp600, Cp800, Cp1000, Cp1500 in self.testCases:
# Cplist = [Cp300, Cp400, Cp500, Cp600, Cp800, Cp1000, Cp1500]
# species = Species(molecule=[Molecule(SMILES=smiles)])
# species.generateResonanceIsomers()
# thermoData = self.oldDatabase.getThermoData(Species(molecule=[species.molecule[0]]))
# molecule = species.molecule[0]
# for mol in species.molecule[1:]:
# thermoData0 = self.oldDatabase.getAllThermoData(Species(molecule=[mol]))[0][0]
# for data in self.oldDatabase.getAllThermoData(Species(molecule=[mol]))[1:]:
# if data.getEnthalpy(298) < thermoData0.getEnthalpy(298):
# thermoData0 = data
# if thermoData0.getEnthalpy(298) < thermoData.getEnthalpy(298):
# thermoData = thermoData0
# molecule = mol
#
# self.assertAlmostEqual(H298, thermoData.getEnthalpy(298) / 4184, places=1, msg="H298 error for {0}".format(smiles))
# self.assertAlmostEqual(S298, thermoData.getEntropy(298) / 4.184, places=1, msg="S298 error for {0}".format(smiles))
# for T, Cp in zip(self.Tlist, Cplist):
# self.assertAlmostEqual(Cp, thermoData.getHeatCapacity(T) / 4.184, places=1, msg="Cp{1} error for {0}".format(smiles, T))
def testParseThermoComments(self):
"""
Test that the ThermoDatabase.extractSourceFromComments function works properly
on various thermo comments.
"""
from rmgpy.thermo import NASA, NASAPolynomial
# Pure group additivity thermo
propane = Species(
index=3,
label="Propane",
thermo=NASA(
polynomials=[
NASAPolynomial(coeffs=[
3.05257, 0.0125099, 3.79386e-05, -5.12022e-08,
1.87065e-11, -14454.2, 10.0672
],
Tmin=(100, 'K'),
Tmax=(986.57, 'K')),
NASAPolynomial(coeffs=[
5.91316, 0.0218763, -8.17661e-06, 1.49855e-09,
-1.05991e-13, -16038.9, -8.86555
],
Tmin=(986.57, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
comment=
"""Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(CsCsRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R)"""
),
molecule=[Molecule(SMILES="CCC")])
source = self.database.extractSourceFromComments(propane)
self.assertTrue(
'GAV' in source,
'Should have found that propane thermo source is GAV.')
self.assertEqual(len(source['GAV']['group']), 2)
self.assertEqual(len(source['GAV']['other']), 1)
self.assertEqual(len(source['GAV']['gauche']), 2)
# Pure library thermo
dipk = Species(index=1,
label="DIPK",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
3.35002, 0.017618, -2.46235e-05, 1.7684e-08,
-4.87962e-12, 35555.7, 5.75335
],
Tmin=(100, 'K'),
Tmax=(888.28, 'K')),
NASAPolynomial(coeffs=[
6.36001, 0.00406378, -1.73509e-06, 5.05949e-10,
-4.49975e-14, 35021, -8.41155
],
Tmin=(888.28, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
comment="""Thermo library: DIPK"""),
molecule=[Molecule(SMILES="CC(C)C(=O)C(C)C")])
source = self.database.extractSourceFromComments(dipk)
self.assertTrue('Library' in source)
# Mixed library and HBI thermo
dipk_rad = Species(
index=4,
label="R_tert",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
2.90061, 0.0298018, -7.06268e-05, 6.9636e-08, -2.42414e-11,
54431, 5.44492
],
Tmin=(100, 'K'),
Tmax=(882.19, 'K')),
NASAPolynomial(coeffs=[
6.70999, 0.000201027, 6.65617e-07, -7.99543e-11,
4.08721e-15, 54238.6, -9.73662
],
Tmin=(882.19, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
comment="""Thermo library: DIPK + radical(C2CJCHO)"""),
molecule=[
Molecule(SMILES="C[C](C)C(=O)C(C)C"),
Molecule(SMILES="CC(C)=C([O])C(C)C")
])
source = self.database.extractSourceFromComments(dipk_rad)
self.assertTrue('Library' in source)
self.assertTrue('GAV' in source)
self.assertEqual(len(source['GAV']['radical']), 1)
# Pure QM thermo
cineole = Species(
index=6,
label="Cineole",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
-0.324129, 0.0619667, 9.71008e-05, -1.60598e-07,
6.28285e-11, -38699.9, 29.3686
],
Tmin=(100, 'K'),
Tmax=(985.52, 'K')),
NASAPolynomial(coeffs=[
20.6043, 0.0586913, -2.22152e-05, 4.19949e-09,
-3.06046e-13, -46791, -91.4152
],
Tmin=(985.52, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
comment="""QM MopacMolPM3 calculation attempt 1"""),
molecule=[Molecule(SMILES="CC12CCC(CC1)C(C)(C)O2")])
source = self.database.extractSourceFromComments(cineole)
self.assertTrue('QM' in source)
# Mixed QM and HBI thermo
cineole_rad = Species(
index=7,
label="CineoleRad",
thermo=NASA(
polynomials=[
NASAPolynomial(coeffs=[
-0.2897, 0.0627717, 8.63299e-05, -1.47868e-07,
5.81665e-11, -14017.6, 31.0266
],
Tmin=(100, 'K'),
Tmax=(988.76, 'K')),
NASAPolynomial(coeffs=[
20.4836, 0.0562555, -2.13903e-05, 4.05725e-09,
-2.96023e-13, -21915, -88.1205
],
Tmin=(988.76, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
comment=
"""QM MopacMolPM3 calculation attempt 1 + radical(Cs_P)"""),
molecule=[Molecule(SMILES="[CH2]C12CCC(CC1)C(C)(C)O2")])
source = self.database.extractSourceFromComments(cineole_rad)
self.assertTrue('QM' in source)
self.assertTrue('GAV' in source)
self.assertEqual(len(source['GAV']['radical']), 1)
# No thermo comments
other = Species(
index=7,
label="CineoleRad",
thermo=NASA(
polynomials=[
NASAPolynomial(coeffs=[
-0.2897, 0.0627717, 8.63299e-05, -1.47868e-07,
5.81665e-11, -14017.6, 31.0266
],
Tmin=(100, 'K'),
Tmax=(988.76, 'K')),
NASAPolynomial(coeffs=[
20.4836, 0.0562555, -2.13903e-05, 4.05725e-09,
-2.96023e-13, -21915, -88.1205
],
Tmin=(988.76, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
),
molecule=[Molecule(SMILES="[CH2]C12CCC(CC1)C(C)(C)O2")])
# Function should complain if there's no thermo comments
self.assertRaises(self.database.extractSourceFromComments(cineole_rad))
# Check a dummy species that has plus and minus thermo group contributions
polycyclic = Species(
index=7,
label="dummy",
thermo=NASA(
polynomials=[
NASAPolynomial(coeffs=[
-0.2897, 0.0627717, 8.63299e-05, -1.47868e-07,
5.81665e-11, -14017.6, 31.0266
],
Tmin=(100, 'K'),
Tmax=(988.76, 'K')),
NASAPolynomial(coeffs=[
20.4836, 0.0562555, -2.13903e-05, 4.05725e-09,
-2.96023e-13, -21915, -88.1205
],
Tmin=(988.76, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
comment=
"""Thermo group additivity estimation: group(Cs-CsCsHH) + group(Cs-CsCsHH) - ring(Benzene)"""
),
molecule=[Molecule(SMILES="[CH2]C12CCC(CC1)C(C)(C)O2")])
source = self.database.extractSourceFromComments(polycyclic)
self.assertTrue('GAV' in source)
self.assertEqual(source['GAV']['ring'][0][1],
-1) # the weight of benzene contribution should be -1
self.assertEqual(
source['GAV']['group'][0][1],
2) # weight of the group(Cs-CsCsHH) conbtribution should be 2
class TestThermoDatabase(unittest.TestCase):
"""
Contains unit tests of the ThermoDatabase class.
"""
# Only load these once to save time
database = ThermoDatabase()
database.load(os.path.join(settings['database.directory'], 'thermo'))
# oldDatabase = ThermoDatabase()
# oldDatabase.loadOld(os.path.join(settings['database.directory'], '../output/RMG_database'))
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.database = self.__class__.database
# self.oldDatabase = self.__class__.oldDatabase
self.Tlist = [300, 400, 500, 600, 800, 1000, 1500]
self.testCases = [
# SMILES symm H298 S298 Cp300 Cp400 Cp500 Cp600 Cp800 Cp1000 Cp1500
# 1,3-hexadiene decomposition products
[
'C=CC=CCC', 3, 13.45, 86.37, 29.49, 37.67, 44.54, 50.12, 58.66,
64.95, 74.71
],
[
'[CH]=CC=CCC', 3, 72.55, 87.76, 29.30, 36.92, 43.18, 48.20,
55.84, 61.46, 70.18
],
[
'C=[C]C=CCC', 3, 61.15, 87.08, 29.68, 36.91, 43.03, 48.11,
55.96, 61.78, 71.54
],
[
'C=C[C]=CCC', 3, 61.15, 87.08, 29.68, 36.91, 43.03, 48.11,
55.96, 61.78, 71.54
],
[
'C=CC=[C]CC', 3, 70.35, 88.18, 29.15, 36.46, 42.6, 47.6, 55.32,
61.04, 69.95
],
[
'C=CC=C[CH]C', 6, 38.24, 84.41, 27.79, 35.46, 41.94, 47.43,
55.74, 61.92, 71.86
],
[
'C=CC=CC[CH2]', 2, 62.45, 89.78, 28.72, 36.31, 42.63, 47.72,
55.50, 61.21, 70.05
],
[
'[CH3]', 6, 34.81, 46.37, 9.14, 10.18, 10.81, 11.34, 12.57,
13.71, 15.2
],
[
'C=CC=C[CH2]', 2, 46.11, 75.82, 22.54, 28.95, 34.24, 38.64,
45.14, 49.97, 57.85
],
[
'[CH2]C', 6, 28.6, 59.87, 11.73, 14.47, 17.05, 19.34, 23.02,
25.91, 31.53
],
[
'C=CC=[CH]', 1, 85.18, 69.37, 18.93, 23.55, 27.16, 29.92,
34.02, 37.03, 41.81
],
[
'C=[CH]', 1, 71.62, 56.61, 10.01, 11.97, 13.66, 15.08, 17.32,
19.05, 21.85
],
[
'[CH]=CCC', 3, 58.99, 75.0, 20.38, 25.34, 29.68, 33.36, 39.14,
43.48, 50.22
],
# Cyclic Structures
[
'C1CCCCC1', 12, -29.45, 69.71, 27.20, 37.60, 46.60, 54.80,
67.50, 76.20, 88.50
],
[
'C1CCC1', 8, 6.51, 63.35, 17.39, 23.91, 29.86, 34.76, 42.40,
47.98, 56.33
],
[
'C1C=CC=C1', 2, 32.5, 65.5, 18.16, 24.71, 30.25, 34.7, 41.25,
45.83, 52.61
],
]
@work_in_progress
def testNewThermoGeneration(self):
"""
Test that the new ThermoDatabase generates appropriate thermo data.
"""
for smiles, symm, H298, S298, Cp300, Cp400, Cp500, Cp600, Cp800, Cp1000, Cp1500 in self.testCases:
Cplist = [Cp300, Cp400, Cp500, Cp600, Cp800, Cp1000, Cp1500]
molecule = Molecule(SMILES=smiles)
species = Species(molecule=molecule)
species.generateResonanceIsomers()
species.molecule[0]
thermoData = self.database.getThermoDataFromGroups(species)
molecule = species.molecule[0]
for mol in species.molecule[1:]:
thermoData0 = self.database.getAllThermoData(
Species(molecule=[mol]))[0][0]
for data in self.database.getAllThermoData(
Species(molecule=[mol]))[1:]:
if data.getEnthalpy(298) < thermoData0.getEnthalpy(298):
thermoData0 = data
if thermoData0.getEnthalpy(298) < thermoData.getEnthalpy(298):
thermoData = thermoData0
molecule = mol
self.assertAlmostEqual(H298,
thermoData.getEnthalpy(298) / 4184,
places=1,
msg="H298 error for {0}".format(smiles))
self.assertAlmostEqual(S298,
thermoData.getEntropy(298) / 4.184,
places=1,
msg="S298 error for {0}".format(smiles))
for T, Cp in zip(self.Tlist, Cplist):
self.assertAlmostEqual(Cp,
thermoData.getHeatCapacity(T) / 4.184,
places=1,
msg="Cp{1} error for {0}".format(
smiles, T))
def testSymmetryContributionRadicals(self):
"""
Test that the symmetry contribution is correctly added for radicals
estimated via the HBI method.
"""
spc = Species(molecule=[Molecule().fromSMILES('[CH3]')])
thermoData_lib = self.database.getThermoDataFromLibraries(spc)[0]
thermoData_ga = self.database.getThermoDataFromGroups(spc)
self.assertAlmostEqual(thermoData_lib.getEntropy(298.),
thermoData_ga.getEntropy(298.), 0)
@work_in_progress
def testSymmetryNumberGeneration(self):
"""
Test we generate symmetry numbers correctly.
This uses the new thermo database to generate the H298, used
to select the stablest resonance isomer.
"""
for smiles, symm, H298, S298, Cp300, Cp400, Cp500, Cp600, Cp800, Cp1000, Cp1500 in self.testCases:
molecule = Molecule(SMILES=smiles)
species = Species(molecule=molecule)
species.generateResonanceIsomers()
thermoData = self.database.getThermoDataFromGroups(
Species(molecule=[species.molecule[0]]))
# pick the molecule with lowest H298
molecule = species.molecule[0]
for mol in species.molecule[1:]:
thermoData0 = self.database.getAllThermoData(
Species(molecule=[mol]))[0][0]
for data in self.database.getAllThermoData(
Species(molecule=[mol]))[1:]:
if data.getEnthalpy(298) < thermoData0.getEnthalpy(298):
thermoData0 = data
if thermoData0.getEnthalpy(298) < thermoData.getEnthalpy(298):
thermoData = thermoData0
molecule = mol
self.assertEqual(
molecule.calculateSymmetryNumber(),
symm,
msg="Symmetry number error for {0}".format(smiles))